src/jalview/appletgui/AnnotationColumnChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.datamodel.AlignmentAnnotation;
  24 import jalview.datamodel.ColumnSelection;
  25 import jalview.schemes.AnnotationColourGradient;
  26 import jalview.util.MessageManager;
  27 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.CardLayout;
  31 import java.awt.Checkbox;
  32 import java.awt.Choice;
  33 import java.awt.Color;
  34 import java.awt.Dimension;
  35 import java.awt.Frame;
  36 import java.awt.Panel;
  37 import java.awt.TextField;
  38 import java.awt.event.ActionEvent;
  39 import java.awt.event.ActionListener;
  40 import java.awt.event.AdjustmentEvent;
  41 import java.awt.event.AdjustmentListener;
  42 import java.awt.event.ItemEvent;
  43 import java.awt.event.ItemListener;
  44 import java.awt.event.MouseAdapter;
  45 import java.awt.event.MouseEvent;
  46 import java.awt.event.MouseListener;
  47 import java.awt.event.TextEvent;
  48 import java.awt.event.TextListener;
  49 import java.util.Iterator;
  50 import java.util.Vector;
  51
  52 //import javax.swing.JPanel;
  53
  54 //import net.miginfocom.swing.MigLayout;
  55
  56 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  57         ActionListener, AdjustmentListener, ItemListener, MouseListener
  58 {
  59
  60   private Choice annotations = new Choice();
  61
  62   private Panel actionPanel = new Panel();
  63
  64   private TitledPanel thresholdPanel = new TitledPanel();
  65
  66   private Panel switchableViewsPanel = new Panel(new CardLayout());
  67
  68   private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
  69           .getLayout());
  70
  71   private Panel noGraphFilterView = new Panel();
  72
  73   private Panel graphFilterView = new Panel();
  74
  75   private Panel annotationComboBoxPanel = new Panel();
  76
  77   private BorderLayout borderLayout1 = new BorderLayout();
  78
  79   private BorderLayout gBorderLayout = new BorderLayout();
  80
  81   private BorderLayout ngBorderLayout = new BorderLayout();
  82
  83   private Choice threshold = new Choice();
  84
  85   private StructureFilterPanel gStructureFilterPanel;
  86
  87   private StructureFilterPanel ngStructureFilterPanel;
  88
  89   private StructureFilterPanel currentStructureFilterPanel;
  90
  91   private SearchPanel currentSearchPanel;
  92
  93   private SearchPanel gSearchPanel;
  94
  95   private SearchPanel ngSearchPanel;
  96
  97   private FurtherActionPanel currentFurtherActionPanel;
  98
  99   private FurtherActionPanel gFurtherActionPanel;
 100
 101   private FurtherActionPanel ngFurtherActionPanel;
 102
 103   public static final int ACTION_OPTION_SELECT = 1;
 104
 105   public static int ACTION_OPTION_HIDE = 2;
 106
 107   public static String NO_GRAPH_VIEW = "0";
 108
 109   public static String GRAPH_VIEW = "1";
 110
 111   private int actionOption = ACTION_OPTION_SELECT;
 112
 113   private ColumnSelection oldColumnSelection;
 114
 115   public AnnotationColumnChooser()
 116   {
 117     try
 118     {
 119       jbInit();
 120     } catch (Exception ex)
 121     {
 122       ex.printStackTrace();
 123     }
 124   }
 125
 126   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
 127   {
 128     super(av, ap);
 129     frame = new Frame();
 130     frame.add(this);
 131     jalview.bin.JalviewLite.addFrame(frame,
 132             MessageManager.getString("label.select_by_annotation"), 520,
 133             215);
 134
 135     slider.addAdjustmentListener(this);
 136     slider.addMouseListener(this);
 137
 138     AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
 139     if (anns == null)
 140     {
 141       return;
 142     }
 143     setOldColumnSelection(av.getColumnSelection());
 144     adjusting = true;
 145     Vector<String> list = new Vector<String>();
 146     int index = 1;
 147     for (int i = 0; i < anns.length; i++)
 148     {
 149       String label = anns[i].label;
 150       if (anns[i].sequenceRef != null)
 151       {
 152         label = label + "_" + anns[i].sequenceRef.getName();
 153       }
 154       if (!list.contains(label))
 155       {
 156         list.addElement(label);
 157       }
 158       else
 159       {
 160         list.addElement(label + "_" + (index++));
 161       }
 162     }
 163
 164     for (int i = 0; i < list.size(); i++)
 165     {
 166       annotations.addItem(list.elementAt(i).toString());
 167     }
 168
 169     populateThresholdComboBox(threshold);
 170
 171     // restore Object state from the previous session if one exists
 172     if (av.getAnnotationColumnSelectionState() != null)
 173     {
 174       currentSearchPanel = av.getAnnotationColumnSelectionState()
 175               .getCurrentSearchPanel();
 176       currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
 177               .getCurrentStructureFilterPanel();
 178       annotations.select(av.getAnnotationColumnSelectionState()
 179               .getAnnotations().getSelectedIndex());
 180       threshold.select(av.getAnnotationColumnSelectionState()
 181               .getThreshold().getSelectedIndex());
 182       actionOption = av.getAnnotationColumnSelectionState()
 183               .getActionOption();
 184     }
 185
 186     try
 187     {
 188       jbInit();
 189     } catch (Exception ex)
 190     {
 191     }
 192     adjusting = false;
 193
 194     updateView();
 195     frame.invalidate();
 196     frame.pack();
 197   }
 198
 199   private void jbInit() throws Exception
 200   {
 201     ok.setLabel(MessageManager.getString("action.ok"));
 202
 203     cancel.setLabel(MessageManager.getString("action.cancel"));
 204
 205     thresholdValue.setEnabled(false);
 206     thresholdValue.setColumns(7);
 207
 208     ok.addActionListener(this);
 209     cancel.addActionListener(this);
 210     annotations.addItemListener(this);
 211     thresholdValue.addActionListener(this);
 212     threshold.addItemListener(this);
 213
 214     slider.setBackground(Color.white);
 215     slider.setEnabled(false);
 216     slider.setPreferredSize(new Dimension(100, 32));
 217
 218     thresholdPanel.setBackground(Color.white);
 219     // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 220     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 221
 222     percentThreshold.setLabel("As percentage");
 223     percentThreshold.addItemListener(this);
 224
 225     actionPanel.setBackground(Color.white);
 226     // actionPanel.setFont(JvSwingUtils.getLabelFont());
 227
 228     graphFilterView.setLayout(gBorderLayout);
 229     graphFilterView.setBackground(Color.white);
 230
 231     noGraphFilterView.setLayout(ngBorderLayout);
 232     noGraphFilterView.setBackground(Color.white);
 233
 234     annotationComboBoxPanel.setBackground(Color.white);
 235     // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 236
 237     gSearchPanel = new SearchPanel(this);
 238     ngSearchPanel = new SearchPanel(this);
 239     gFurtherActionPanel = new FurtherActionPanel(this);
 240     ngFurtherActionPanel = new FurtherActionPanel(this);
 241     gStructureFilterPanel = new StructureFilterPanel(this);
 242     ngStructureFilterPanel = new StructureFilterPanel(this);
 243
 244     thresholdPanel.setTitle("Threshold Filter");
 245     thresholdPanel.add(percentThreshold);
 246     thresholdPanel.add(getThreshold());
 247     thresholdPanel.add(slider);
 248     thresholdPanel.add(thresholdValue);
 249
 250     actionPanel.add(ok);
 251     actionPanel.add(cancel);
 252
 253     Panel staticPanel = new Panel();
 254     staticPanel.setLayout(new BorderLayout());
 255     staticPanel.setBackground(Color.white);
 256
 257     staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
 258     staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
 259
 260     graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
 261     graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
 262     graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
 263
 264     noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
 265     noGraphFilterView.add(ngStructureFilterPanel,
 266             java.awt.BorderLayout.CENTER);
 267     noGraphFilterView.add(ngFurtherActionPanel,
 268             java.awt.BorderLayout.CENTER);
 269
 270     annotationComboBoxPanel.add(getAnnotations());
 271     switchableViewsPanel.add(noGraphFilterView,
 272             AnnotationColumnChooser.NO_GRAPH_VIEW);
 273     switchableViewsPanel.add(graphFilterView,
 274             AnnotationColumnChooser.GRAPH_VIEW);
 275
 276     this.setLayout(borderLayout1);
 277     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 278     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 279     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 280
 281     selectedAnnotationChanged();
 282     this.validate();
 283   }
 284
 285   @Override
 286   @SuppressWarnings("unchecked")
 287   public void reset()
 288   {
 289     if (this.getOldColumnSelection() != null)
 290     {
 291       av.getColumnSelection().clear();
 292
 293       if (av.getAnnotationColumnSelectionState() != null)
 294       {
 295         ColumnSelection oldSelection = av
 296                 .getAnnotationColumnSelectionState()
 297                 .getOldColumnSelection();
 298         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 299                 && !oldSelection.getHiddenColumns().isEmpty())
 300         {
 301           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 302                   .iterator(); itr.hasNext();)
 303           {
 304             int positions[] = itr.next();
 305             av.hideColumns(positions[0], positions[1]);
 306           }
 307         }
 308         av.setColumnSelection(oldSelection);
 309       }
 310       ap.paintAlignment(true);
 311     }
 312
 313   }
 314
 315   @Override
 316   public void adjustmentValueChanged(AdjustmentEvent evt)
 317   {
 318     if (!adjusting)
 319     {
 320       thresholdValue.setText((slider.getValue() / 1000f) + "");
 321       valueChanged(!sliderDragging);
 322     }
 323   }
 324
 325   protected void addSliderMouseListeners()
 326   {
 327
 328     slider.addMouseListener(new MouseAdapter()
 329     {
 330       @Override
 331       public void mousePressed(MouseEvent e)
 332       {
 333         sliderDragging = true;
 334         super.mousePressed(e);
 335       }
 336
 337       @Override
 338       public void mouseDragged(MouseEvent e)
 339       {
 340         sliderDragging = true;
 341         super.mouseDragged(e);
 342       }
 343
 344       @Override
 345       public void mouseReleased(MouseEvent evt)
 346       {
 347         if (sliderDragging)
 348         {
 349           sliderDragging = false;
 350           valueChanged(true);
 351         }
 352         ap.paintAlignment(true);
 353       }
 354     });
 355   }
 356
 357   @Override
 358   public void valueChanged(boolean updateAllAnnotation)
 359   {
 360     if (slider.isEnabled())
 361     {
 362       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 363       updateView();
 364       ap.paintAlignment(false);
 365     }
 366   }
 367
 368   public Choice getThreshold()
 369   {
 370     return threshold;
 371   }
 372
 373   public void setThreshold(Choice threshold)
 374   {
 375     this.threshold = threshold;
 376   }
 377
 378   public Choice getAnnotations()
 379   {
 380     return annotations;
 381   }
 382
 383   public void setAnnotations(Choice annotations)
 384   {
 385     this.annotations = annotations;
 386   }
 387
 388   @Override
 389   public void updateView()
 390   {
 391     // Check if combobox is still adjusting
 392     if (adjusting)
 393     {
 394       return;
 395     }
 396
 397     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 398     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 399             .getSelectedIndex()]);
 400
 401     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 402             .getSelectedIndex());
 403
 404     slider.setEnabled(true);
 405     thresholdValue.setEnabled(true);
 406
 407     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 408     {
 409       slider.setEnabled(false);
 410       thresholdValue.setEnabled(false);
 411       thresholdValue.setText("");
 412       // build filter params
 413     }
 414     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 415     {
 416       if (getCurrentAnnotation().threshold == null)
 417       {
 418         getCurrentAnnotation()
 419                 .setThreshold(
 420                         new jalview.datamodel.GraphLine(
 421                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 422                                 "Threshold", Color.black));
 423       }
 424
 425       adjusting = true;
 426       float range = getCurrentAnnotation().graphMax * 1000
 427               - getCurrentAnnotation().graphMin * 1000;
 428
 429       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 430       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 431       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 432       setThresholdValueText();
 433       // slider.setMajorTickSpacing((int) (range / 10f));
 434       slider.setEnabled(true);
 435       thresholdValue.setEnabled(true);
 436       adjusting = false;
 437
 438       // build filter params
 439       filterParams
 440               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 441       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 442       {
 443         filterParams
 444                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 445
 446         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 447         {
 448           filterParams
 449                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 450         }
 451         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 452         {
 453           filterParams
 454                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 455         }
 456       }
 457     }
 458
 459     if (currentStructureFilterPanel != null)
 460     {
 461       if (currentStructureFilterPanel.alphaHelix.getState())
 462       {
 463         filterParams.setFilterAlphaHelix(true);
 464       }
 465       if (currentStructureFilterPanel.betaStrand.getState())
 466       {
 467         filterParams.setFilterBetaSheet(true);
 468       }
 469       if (currentStructureFilterPanel.turn.getState())
 470       {
 471         filterParams.setFilterTurn(true);
 472       }
 473     }
 474
 475     if (currentSearchPanel != null)
 476     {
 477
 478       if (!currentSearchPanel.searchBox.getText().isEmpty())
 479       {
 480         currentSearchPanel.description.setEnabled(true);
 481         currentSearchPanel.displayName.setEnabled(true);
 482         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 483         if (currentSearchPanel.displayName.getState())
 484         {
 485           filterParams
 486                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 487         }
 488         if (currentSearchPanel.description.getState())
 489         {
 490           filterParams
 491                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 492         }
 493       }
 494       else
 495       {
 496         currentSearchPanel.description.setEnabled(false);
 497         currentSearchPanel.displayName.setEnabled(false);
 498       }
 499     }
 500
 501     av.getColumnSelection().filterAnnotations(
 502             getCurrentAnnotation().annotations, filterParams);
 503
 504     av.showAllHiddenColumns();
 505     if (getActionOption() == ACTION_OPTION_HIDE)
 506     {
 507       av.hideSelectedColumns();
 508     }
 509
 510     filterParams = null;
 511     av.setAnnotationColumnSelectionState(this);
 512     ap.paintAlignment(true);
 513   }
 514
 515   public ColumnSelection getOldColumnSelection()
 516   {
 517     return oldColumnSelection;
 518   }
 519
 520   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 521   {
 522     if (currentColumnSelection != null)
 523     {
 524       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 525     }
 526   }
 527
 528   public FurtherActionPanel getCurrentFutherActionPanel()
 529   {
 530     return currentFurtherActionPanel;
 531   }
 532
 533   public void setCurrentFutherActionPanel(
 534           FurtherActionPanel currentFutherActionPanel)
 535   {
 536     this.currentFurtherActionPanel = currentFutherActionPanel;
 537   }
 538
 539   public SearchPanel getCurrentSearchPanel()
 540   {
 541     return currentSearchPanel;
 542   }
 543
 544   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 545   {
 546     this.currentSearchPanel = currentSearchPanel;
 547   }
 548
 549   public int getActionOption()
 550   {
 551     return actionOption;
 552   }
 553
 554   public void setActionOption(int actionOption)
 555   {
 556     this.actionOption = actionOption;
 557   }
 558
 559   public StructureFilterPanel getCurrentStructureFilterPanel()
 560   {
 561     return currentStructureFilterPanel;
 562   }
 563
 564   public void setCurrentStructureFilterPanel(
 565           StructureFilterPanel currentStructureFilterPanel)
 566   {
 567     this.currentStructureFilterPanel = currentStructureFilterPanel;
 568   }
 569
 570   @Override
 571   public void itemStateChanged(ItemEvent e)
 572   {
 573     if (e.getSource() == annotations)
 574     {
 575       selectedAnnotationChanged();
 576     }
 577     else if (e.getSource() == threshold)
 578     {
 579       threshold_actionPerformed(null);
 580     }
 581     else if (e.getSource() == percentThreshold)
 582     {
 583       if (!adjusting)
 584       {
 585         percentageValue_actionPerformed();
 586       }
 587
 588     }
 589   }
 590
 591   public void selectedAnnotationChanged()
 592   {
 593     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 594     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 595             .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH)
 596     {
 597       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 598     }
 599
 600     gSearchPanel.syncState();
 601     gFurtherActionPanel.syncState();
 602     gStructureFilterPanel.syncState();
 603
 604     ngSearchPanel.syncState();
 605     ngFurtherActionPanel.syncState();
 606     ngStructureFilterPanel.syncState();
 607
 608     switchableViewsLayout.show(switchableViewsPanel, currentView);
 609     updateView();
 610   }
 611
 612   public class FurtherActionPanel extends Panel implements ItemListener
 613   {
 614     private AnnotationColumnChooser aColChooser;
 615
 616     private Choice furtherAction = new Choice();
 617
 618     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 619     {
 620       this.aColChooser = aColChooser;
 621       furtherAction.addItem("Select");
 622       furtherAction.addItem("Hide");
 623       furtherAction.addItemListener(this);
 624       syncState();
 625
 626       // this.setTitle("Filter Actions");
 627       // this.setFont(JvSwingUtils.getLabelFont());
 628
 629       this.add(furtherAction);
 630     }
 631
 632     public void syncState()
 633     {
 634       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 635       {
 636         furtherAction.select("Hide");
 637       }
 638       else
 639       {
 640         furtherAction.select("Select");
 641       }
 642     }
 643
 644     @Override
 645     public void itemStateChanged(ItemEvent e)
 646     {
 647       aColChooser.setCurrentFutherActionPanel(this);
 648       if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
 649       {
 650         setActionOption(ACTION_OPTION_SELECT);
 651         updateView();
 652       }
 653       else
 654       {
 655         setActionOption(ACTION_OPTION_HIDE);
 656         updateView();
 657       }
 658
 659     }
 660   }
 661
 662   public class StructureFilterPanel extends TitledPanel implements
 663           ItemListener
 664   {
 665     private AnnotationColumnChooser aColChooser;
 666
 667     private Checkbox alphaHelix = new Checkbox();
 668
 669     private Checkbox betaStrand = new Checkbox();
 670
 671     private Checkbox turn = new Checkbox();
 672
 673     private Checkbox all = new Checkbox();
 674
 675     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 676     {
 677       this.aColChooser = aColChooser;
 678
 679       alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
 680       alphaHelix.setBackground(Color.white);
 681
 682       alphaHelix.addItemListener(this);
 683
 684       betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
 685       betaStrand.setBackground(Color.white);
 686       betaStrand.addItemListener(this);
 687
 688       turn.setLabel(MessageManager.getString("label.turn"));
 689       turn.setBackground(Color.white);
 690       turn.addItemListener(this);
 691
 692       all.setLabel(MessageManager.getString("label.select_all"));
 693       all.setBackground(Color.white);
 694       all.addItemListener(this);
 695
 696       this.setBackground(Color.white);
 697       this.setTitle("Structure Filter");
 698       // this.setFont(JvSwingUtils.getLabelFont());
 699
 700       this.add(all);
 701       this.add(alphaHelix);
 702       this.add(betaStrand);
 703       this.add(turn);
 704     }
 705
 706     public void alphaHelix_actionPerformed()
 707     {
 708       updateSelectAllState();
 709       aColChooser.setCurrentStructureFilterPanel(this);
 710       aColChooser.updateView();
 711     }
 712
 713     public void betaStrand_actionPerformed()
 714     {
 715       updateSelectAllState();
 716       aColChooser.setCurrentStructureFilterPanel(this);
 717       aColChooser.updateView();
 718     }
 719
 720     public void turn_actionPerformed()
 721     {
 722       updateSelectAllState();
 723       aColChooser.setCurrentStructureFilterPanel(this);
 724       aColChooser.updateView();
 725     }
 726
 727     public void all_actionPerformed()
 728     {
 729       if (all.getState())
 730       {
 731         alphaHelix.setState(true);
 732         betaStrand.setState(true);
 733         turn.setState(true);
 734       }
 735       else
 736       {
 737         alphaHelix.setState(false);
 738         betaStrand.setState(false);
 739         turn.setState(false);
 740       }
 741       aColChooser.setCurrentStructureFilterPanel(this);
 742       aColChooser.updateView();
 743     }
 744
 745     public void updateSelectAllState()
 746     {
 747       if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
 748       {
 749         all.setState(true);
 750       }
 751       else
 752       {
 753         all.setState(false);
 754       }
 755     }
 756
 757     public void syncState()
 758     {
 759       StructureFilterPanel sfp = aColChooser
 760               .getCurrentStructureFilterPanel();
 761       if (sfp != null)
 762       {
 763         alphaHelix.setState(sfp.alphaHelix.getState());
 764         betaStrand.setState(sfp.betaStrand.getState());
 765         turn.setState(sfp.turn.getState());
 766         if (sfp.all.getState())
 767         {
 768           all.setState(true);
 769           alphaHelix.setState(true);
 770           betaStrand.setState(true);
 771           turn.setState(true);
 772         }
 773       }
 774
 775     }
 776
 777     @Override
 778     public void itemStateChanged(ItemEvent e)
 779     {
 780       if (e.getSource() == alphaHelix)
 781       {
 782         alphaHelix_actionPerformed();
 783       }
 784       else if (e.getSource() == betaStrand)
 785       {
 786         betaStrand_actionPerformed();
 787       }
 788       else if (e.getSource() == turn)
 789       {
 790         turn_actionPerformed();
 791       }
 792       else if (e.getSource() == all)
 793       {
 794         all_actionPerformed();
 795       }
 796     }
 797   }
 798
 799   public class SearchPanel extends TitledPanel implements ItemListener
 800   {
 801     private AnnotationColumnChooser aColChooser;
 802
 803     private Checkbox displayName = new Checkbox();
 804
 805     private Checkbox description = new Checkbox();
 806
 807     private TextField searchBox = new TextField(10);
 808
 809     public SearchPanel(AnnotationColumnChooser aColChooser)
 810     {
 811
 812       this.aColChooser = aColChooser;
 813       searchBox.addTextListener(new TextListener()
 814       {
 815
 816         @Override
 817         public void textValueChanged(TextEvent e)
 818         {
 819           searchStringAction();
 820
 821         }
 822
 823       });
 824
 825       displayName.setLabel(MessageManager.getString("label.label"));
 826       displayName.setEnabled(false);
 827       displayName.addItemListener(this);
 828
 829       description.setLabel(MessageManager.getString("label.description"));
 830       description.setEnabled(false);
 831       description.addItemListener(this);
 832       this.setTitle("Search Filter");
 833       // this.setFont(JvSwingUtils.getLabelFont());
 834
 835       syncState();
 836       this.add(searchBox);
 837       this.add(displayName);
 838       this.add(description);
 839     }
 840
 841     public void displayNameCheckboxAction()
 842     {
 843       aColChooser.setCurrentSearchPanel(this);
 844       aColChooser.updateView();
 845     }
 846
 847     public void discriptionCheckboxAction()
 848     {
 849       aColChooser.setCurrentSearchPanel(this);
 850       aColChooser.updateView();
 851     }
 852
 853     public void searchStringAction()
 854     {
 855       aColChooser.setCurrentSearchPanel(this);
 856       aColChooser.updateView();
 857     }
 858
 859     public void syncState()
 860     {
 861       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 862       if (sp != null)
 863       {
 864         description.setEnabled(sp.description.isEnabled());
 865         description.setState(sp.description.getState());
 866
 867         displayName.setEnabled(sp.displayName.isEnabled());
 868         displayName.setState(sp.displayName.getState());
 869
 870         searchBox.setText(sp.searchBox.getText());
 871       }
 872     }
 873
 874     @Override
 875     public void itemStateChanged(ItemEvent e)
 876     {
 877       if (e.getSource() == displayName)
 878       {
 879         displayNameCheckboxAction();
 880       }
 881       else if (e.getSource() == description)
 882       {
 883         discriptionCheckboxAction();
 884       }
 885
 886     }
 887   }
 888
 889   @Override
 890   public void actionPerformed(ActionEvent evt)
 891   {
 892     if (evt.getSource() == thresholdValue)
 893     {
 894       try
 895       {
 896         float f = new Float(thresholdValue.getText()).floatValue();
 897         slider.setValue((int) (f * 1000));
 898         adjustmentValueChanged(null);
 899       } catch (NumberFormatException ex)
 900       {
 901       }
 902     }
 903
 904     else if (evt.getSource() == ok)
 905     {
 906       ok_actionPerformed(null);
 907     }
 908     else if (evt.getSource() == cancel)
 909     {
 910       cancel_actionPerformed(null);
 911     }
 912     else if (evt.getSource() == thresholdValue)
 913     {
 914       thresholdValue_actionPerformed(null);
 915     }
 916     else
 917     {
 918       updateView();
 919     }
 920   }
 921
 922   @Override
 923   public void mouseClicked(MouseEvent e)
 924   {
 925     // TODO Auto-generated method stub
 926
 927   }
 928
 929   @Override
 930   public void mousePressed(MouseEvent e)
 931   {
 932     if (e.getSource() == slider)
 933     {
 934       updateView();
 935     }
 936
 937   }
 938
 939   @Override
 940   public void mouseReleased(MouseEvent e)
 941   {
 942     if (e.getSource() == slider)
 943     {
 944       updateView();
 945     }
 946   }
 947
 948   @Override
 949   public void mouseEntered(MouseEvent e)
 950   {
 951     if (e.getSource() == slider)
 952     {
 953       updateView();
 954     }
 955   }
 956
 957   @Override
 958   public void mouseExited(MouseEvent e)
 959   {
 960     if (e.getSource() == slider)
 961     {
 962       updateView();
 963     }
 964   }
 965
 966 }